Fiji / ImageJ: Why are there 3 channels while using the Stitching Tool

Dear colleagues,

I am using the stitching tool quite al lot and all of a sudden there appear 3 channels in the stitched image. When I save the image as a jpg-file everything is fine again. But where are these channels coming from?

Did I set up something wrong or edit something?

Best regards,


Just a guess without knowing the stitching algorithm.

You have a Color image which consists of R,G,B values (planes).

These RGB values are splitted (something like the Split Channels command) and stitched seperately.

At the end the channels are fused again.

Dear Bio7,
thanks for your idea and hint. I just checked the settings of my microscope and double-checked via the picture’s information using ImageJ. The stitched images are 8bit greyscale. So this shouldn’t be a problem.

Do you have any other suggestions?

Best regards,

It might be the output of the plugin which in your case has only one channel annotated as channel 3.

However, which plugin do you use by the way?

You might find some documentation or can contact the author directly respectively adress him in this forum.

Good ideas!

I am using the “Grid/Collection stitching” plugin. The interesting question for me is why do I have the 3 channels “all of a sudden”? Is it due to an update or did I accidentally change some properties? (Not that I don’t take care of what I change but this can happen.)

I added a screenshot to make my “problem” or rather question easier to understand.


For me this looks like a composite image of 3 channels. What information do you have when you open the image information of the input and the output (Press the key “i” or invoke menu action Image->Information)?

@StephanPreibisch is the author of the plugin.

Thank you for your reply and suggestion.

The information I get for the single picture is:

And for the stitched image:

I don’t see why it should be 3 channels. Do you have any sugestion?

Thanks also for metnioning the author.

I would contact the author because I don’t know the implementation. Maybee the stitching plugin converts the image in it’s process.

@Bio7: Thank you for your help.